Fig. S1

Fig. S1a

Reads Mapped

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Fig. S1b

Genes detected

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Fig. S1c

Distribution of mean TPM by stage

Fig 1b

Sample Correlation Matrix

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Fig 1d

PCA Plots (using all genes)

3d plot

PC Heatmaps

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Figure S2

PCA Matrix Plot

ChIP-Seq

Figure 3

Fig3a

Max Stage Clusters TPM heatmap

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Undetected genes

GO Enrichment on biolayout clusters

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Figure 4

Cluster Chromosome Count Expected log2FE Adjusted.pvalue
Cluster007 Chr4 99 23.55 2.07 4.772e-35
Cluster023 Chr4 40 6.11 2.71 2.707e-23
Cluster026 Chr4 20 5.03 1.99 1.810e-06
Cluster135 Chr4 9 0.99 3.19 6.997e-07
Cluster086 Chr12 7 0.42 4.05 3.447e-06
Cluster057 Chr23 6 0.69 3.13 1.637e-03

Table showing clusters with significant chr enrichments (adjusted p-value < 0.05 and log2 fold change > 1).

Chr 4 Zinc Finger Genes

Cluster Freq
7 Cluster007 96
23 Cluster023 30
26 Cluster026 18
2 Cluster002 10
135 Cluster135 9
24 Cluster024 5

Table showing the numbers of chromosome 4 zinc finger genes in the biolayout clusters (more than 5 in a cluster).

Chr 4 ZnF enrichment

The table below shows the clusters with enrichments significantly larger than expected by chance for the chromosome 4 zinc finger genes.

Cluster Category Count Expected log2FE pvalue adjusted.pvalue
Cluster007 Chr4ZnF 96 27.28 1.82 4.048e-25 2.429e-24

Table showing clusters with significant enrichments (adjusted p-value < 0.05).

Chr 4 Expression plot

There are 9 clusters with more than 8 genes on chr 4. Need a colour palette for 9 clusters.

Fig4A - ZnF heatmap

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Fig4B - Chr4 tpm heatmap

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Fig4C - ZnF clusters expression profiles

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Fig4D - histograms of ZnF/NLR genes on chr 4

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Histogram showing the distribution of genes in clusters 7, 23, 26 and 135.

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Histogram showing the distribution of NLR genes on chromosome 4 (binwidth = 5 Mb).

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Line graph showing the distribution of ZnF and NLR genes on chromosome 4 (binwidth = 5 Mb).

Fig4E - NLR genes tpm heatmap

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Chr22 Znf genes tpm heatmap

Figure 4 - figure supplement 1

Regional expression

Figure 5

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Get Peaks

## Chr1-29279647-29885073 
## Chr1-40899871-41576486 
## Chr2-4972029-5492830 
## Chr3-33904540-33930645 
## Chr3-33948692-33972567 
## Chr4-28740727-28745253 
## Chr4-31983618-32298331 
## Chr4-40461327-40771283 
## Chr4-45624179-45994340 
## Chr4-46487297-46605977 
## Chr4-50449048-50657318 
## Chr4-50661962-50742100 
## Chr4-51979572-52361891 
## Chr4-53865601-53897347 
## Chr4-59038291-59167419 
## Chr4-59585793-59894990 
## Chr4-63526050-63629909 
## Chr4-64684113-65167069 
## Chr4-65983752-66208723 
## Chr4-69945188-70379008 
## Chr6-39293241-39510839 
## Chr7-72096634-72338230 
## Chr7-73590418-73606060 
## Chr8-16573954-16576906 
## Chr9-7477783-8100425 
## Chr10-18994837-19609041 
## Chr12-2412104-2635423 
## Chr14-11072281-11303764 
## Chr14-33251312-33594799 
## Chr15-15378107-15524111 
## Chr16-11694674-11888570 
## Chr17-46839113-47219486 
## Chr19-20156555-20400250 
## Chr19-40763348-41319041 
## Chr20-3272730-3309124 
## Chr22-895552-1103977 
## Chr22-2126341-2194312 
## Chr22-28909098-29133881 
## Chr23-35954141-36004832 
## Chr23-37221300-37504077 
## Chr23-40277439-40573494 
## Chr24-192921-523267 
## Chr24-3447094-4408464 
## Chr24-6078572-6641761 
## Chr24-29485795-30192806 
## Chr25-12951696-13285349 
## Chr25-34607134-34628832 
## Chr25-34843668-35322690
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Figure 6

Fig6a

Pearson histogram (Paralogues)

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Kernel density estimate of Pearson coefficients between paralogous gene pairs

Fig6b

top10/bottom10 tpm heatmap

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Fig6c-f

scatterplots/point based expression profiles

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DETCT Data

Figure 9-figure supplement 1

DETCT Sample QC plot

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Figure 9-figure supplement 2

DETCT PCA

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Fig.6C

Count bar chart by Stage

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3’ ends

differential transcript usage

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e90 new genes

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Session Info

## R version 3.3.1 (2016-06-21)
## Platform: x86_64-apple-darwin13.4.0 (64-bit)
## Running under: OS X 10.11.6 (El Capitan)
## 
## locale:
## [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
## 
## attached base packages:
##  [1] grid      stats4    parallel  stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] R2HTML_2.3.2               rgl_0.98.1                
##  [3] qvalue_2.6.0               genefilter_1.56.0         
##  [5] DESeq2_1.14.1              SummarizedExperiment_1.4.0
##  [7] htmlTable_1.9              biomaRt_2.30.0            
##  [9] Rgraphviz_2.18.0           gridExtra_2.2.1           
## [11] topGO_2.26.0               SparseM_1.77              
## [13] GO.db_3.4.0                graph_1.52.0              
## [15] cba_0.2-19                 proxy_0.4-16              
## [17] RColorBrewer_1.1-2         plyr_1.8.4                
## [19] GenomicFeatures_1.26.4     AnnotationDbi_1.36.2      
## [21] Biobase_2.34.0             GenomicRanges_1.26.4      
## [23] GenomeInfoDb_1.10.3        IRanges_2.8.2             
## [25] S4Vectors_0.12.2           scales_0.4.1              
## [27] reshape2_1.4.2             ggbio_1.22.4              
## [29] BiocGenerics_0.20.0        ggplot2_2.2.1             
## [31] rprojroot_1.2              knitr_1.16                
## 
## loaded via a namespace (and not attached):
##  [1] bitops_1.0-6                  matrixStats_0.52.2           
##  [3] bit64_0.9-7                   httr_1.2.1                   
##  [5] tools_3.3.1                   backports_1.1.0              
##  [7] R6_2.2.2                      rpart_4.1-11                 
##  [9] Hmisc_4.0-3                   DBI_0.7                      
## [11] lazyeval_0.2.0                colorspace_1.3-2             
## [13] nnet_7.3-12                   GGally_1.3.1                 
## [15] bit_1.1-12                    labeling_0.3                 
## [17] rtracklayer_1.34.2            checkmate_1.8.2              
## [19] RBGL_1.50.0                   stringr_1.2.0                
## [21] digest_0.6.12                 Rsamtools_1.26.2             
## [23] foreign_0.8-69                rmarkdown_1.6                
## [25] XVector_0.14.1                base64enc_0.1-3              
## [27] dichromat_2.0-0               pkgconfig_2.0.1              
## [29] htmltools_0.3.6               highr_0.6                    
## [31] ensembldb_1.6.2               BSgenome_1.42.0              
## [33] htmlwidgets_0.8               rlang_0.1.1                  
## [35] RSQLite_2.0                   BiocInstaller_1.24.0         
## [37] shiny_1.0.3                   jsonlite_1.5                 
## [39] BiocParallel_1.8.2            acepack_1.4.1                
## [41] VariantAnnotation_1.20.3      RCurl_1.95-4.8               
## [43] magrittr_1.5                  Formula_1.2-1                
## [45] Matrix_1.2-10                 Rcpp_0.12.11                 
## [47] munsell_0.4.3                 stringi_1.1.5                
## [49] yaml_2.1.14                   zlibbioc_1.20.0              
## [51] AnnotationHub_2.6.5           blob_1.1.0                   
## [53] lattice_0.20-35               Biostrings_2.42.1            
## [55] splines_3.3.1                 annotate_1.52.1              
## [57] locfit_1.5-9.1                geneplotter_1.52.0           
## [59] XML_3.98-1.9                  evaluate_0.10.1              
## [61] biovizBase_1.22.0             latticeExtra_0.6-28          
## [63] rnaseqVis_0.0.0.9001          data.table_1.10.4            
## [65] httpuv_1.3.3                  gtable_0.2.0                 
## [67] reshape_0.8.6                 mime_0.5                     
## [69] xtable_1.8-2                  survival_2.41-3              
## [71] tibble_1.3.3                  OrganismDbi_1.16.0           
## [73] GenomicAlignments_1.10.1      memoise_1.1.0                
## [75] cluster_2.0.6                 interactiveDisplayBase_1.12.0